Most cathedral NPCs give you only a small part of their dialogue. A good example is Viola, who has many lines that cannot be accessed. So it's hard to tell if actually any NPCs were completely removed.

There are some MSG files for a type of random encounter that was never fully implemented: people from a nearby location who had lots of dialogue, depending on your rep there, could give you news or lead you to their base.

A gang war in the Boneyard, with the Blades as a regular gang instead of a bunch of wimps and Tangler as a big bad boss of the Rippers (you can hear about them in some tell-me-abouts). Related quests to join the Blades, stop the gangs from attacking Adytum, and rescue Zimmerman's son (Jason, not Josh) from the Rippers.

Happy endings for the Followers (with a picture showing an unbroken wall) and the Hub (with a picture showing Iguana Bob), and mutant invasion endings for Junktown (with a picture showing a the super mutant) including the Brotherhood.